5T3O

Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus

Summary for 5T3O

• Entry DOI: 10.2210/pdb5t3o/pdb
• Descriptor: Ribose-phosphate pyrophosphokinase, ADENOSINE-5'-DIPHOSPHATE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase, modpipe model of up q5shu3
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm : Q5SHU3
• Total number of polymer chains: 3
• Total formula weight: 101266.32

Authors

Timofeev, V.I.,Sinitsyna, E.V.,Abramchik, Y.A.,Kostromina, M.A.,Esipov, R.S.,Kuranova, I.P. (deposition date: 2016-08-26, release date: 2017-06-14, Last modification date: 2024-01-17)

Primary citation

Timofeev, V.I.,Sinitsyna, E.V.,Kostromina, M.A.,Muravieva, T.I.,Makarov, D.A.,Mikheeva, O.O.,Kuranova, I.P.,Esipov, R.S.
Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions.
Acta Crystallogr F Struct Biol Commun, 73:369-375, 2017

PubMed Abstract: Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits in T. thermophilus PRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic β-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.

PubMed: 28580926
DOI: 10.1107/S2053230X17007488

Experimental method

X-RAY DIFFRACTION (2.2 Å)